NAME: Andrey Lebedev

AFFILIATION: University of York, UK

CONTACT: lebedev@ysbl.york.ac.uk

TITLE: "Molrep: model correction and molecular replacement"

ABSTRACT: Andrey A Lebedev, Alexei A Vagin and Garib N Murshudov

Modification of the search model is a necessary prerequisite of successful use of molecular replacement (MR) in most cases but the trivial ones (high sequence similarity, good quality of data, one-two molecules in the asymetric unit), There are four structural levels where the model modifications are applicable: primary, secondary structures, domains and oligomers. Points of view differ on how deep the modifications should be. The algorithms built into MOLREP, and the protocols implemented in BALBES, an automated molecular replacement package, utilise a general concept that model modifications should be based on experimental information and accumulated knowledge (i.e. protein data bank) rather than on predictions. This presentation will demonstrate how MOLREP implements this concept in the context of the four structural levels: the modification by sequence; downweighting the contribution of the variable structural motifs; handling the domain and oligomeric structures. In the context of multi-domain and oligomeric structures we will also discuss the refinement of a partial model that could be further used as a new search model, and the domain/subunit search in the masked electron density.